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Detection of human bocaviruses 1 to 4 from nasopharyngeal swab samples collected from patients with respiratory tract infections.

ABSTRACT: Human bocaviruses (HBoV) 1, 2, 3, and 4 (HBoV1-4) were detected in 132 (15.5%), 5 (0.6%), 3 (0.4%), and 5 (0.6%) of 850 nasopharyngeal swab samples collected from children with respiratory tract infections, respectively. Out of the 145 HBoV1-4-positive samples, 62 (42.8%) were codetected with other respiratory viruses.

SUBMITTER: Koseki N

PROVIDER: S-EPMC3372153 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature

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Detection of human bocaviruses 1 to 4 from nasopharyngeal swab samples collected from patients with respiratory tract infections.

Koseki Naoko N Teramoto Shinobu S Kaiho Miki M Gomi-Endo Rika R Yoshioka Mikio M Takahashi Yutaka Y Nakayama Tsuguyo T Sawada Hiroyuki H Konno Mutsuko M Ushijima Hiroshi H Kikuta Hideaki H Ariga Tadashi T Ishiguro Nobuhisa N

Journal of clinical microbiology 20120321 6

Human bocaviruses (HBoV) 1, 2, 3, and 4 (HBoV1-4) were detected in 132 (15.5%), 5 (0.6%), 3 (0.4%), and 5 (0.6%) of 850 nasopharyngeal swab samples collected from children with respiratory tract infections, respectively. Out of the 145 HBoV1-4-positive samples, 62 (42.8%) were codetected with other respiratory viruses. ...[more]

PMID: 22442328

Similar Datasets

Genetic variability of human metapneumo- and bocaviruses in children with respiratory tract infections.

Project description:OBJECTIVES:The genotypic analysis of human metapneumo-(HMPV) and boca-(HBoV) viruses circulating in Greece and their comparison to reference and other clinical strains. DESIGN:Genetic analysis of representative strains over three consecutive winter seasons of the years 2005-2008. SETTING:Representative positive specimens for HMPV and HBoV from paediatric patients of healthcare units and hospitals in Southern Greece with influenza-like illness or other respiratory tract infections. SAMPLE:Seven to ten positive specimens for either HMPV or HBoV from each winter period. In total, 24 specimens positive for HMPV and 26 for HBoV, respectively. MAIN OUTCOME MEASURES:Sequence diversity of HMPV and HBoV strains by sequencing the complete G and VP1/VP2 genes, respectively. RESULTS:In total, 24 HMPV strains were found to have a 92-100% nucleotide and a 85.9-100% amino acid identity. Phylogenetic analysis based on the number of amino acid differences, revealed circulation of 4 different subclusters belonging to genetic lineage B2. Similarly, analysis of 26 HBoV strains indicated that 22 clustered within genotype St2, 2 into genotype St1 and the remaining 2 formed a third cluster derived from potential recombination between different St1 genotype strains. St2 HBoV genotype was observed throughout the whole observation period whereas St1 only during the second and the third winter period. Higher levels of heterogeneity were observed between HMPV compared to HBoV strains. CONCLUSIONS:Phylogenetic analysis revealed circulation of one single lineage (B2) for HMPV viruses and predominance of St2 genotype for HBoV viruses. A possible recombination between St1 genotype strains of HBoV was observed.

| S-EPMC4177804 | biostudies-literature

Detection of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) in outpatients: A multicenter comparison of self-collected saline gargle, oral swab, and combined oral-anterior nasal swab to a provider collected nasopharyngeal swab.

Project description:BackgroundWidespread testing for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) is necessary to curb the spread of coronavirus disease 2019 (COVID-19), but testing is undermined when the only option is a nasopharyngeal swab. Self-collected swab techniques can overcome many of the disadvantages of a nasopharyngeal swab, but they require evaluation.MethodsThree self-collected non-nasopharyngeal swab techniques (saline gargle, oral swab and combined oral-anterior nasal swab) were compared to a nasopharyngeal swab for SARS-CoV-2 detection at multiple COVID-19 assessment centers in Toronto, Canada. The performance characteristics of each test were assessed.ResultsThe adjusted sensitivity of the saline gargle was 0.90 (95% CI 0.86-0.94), the oral swab was 0.82 (95% CI, 0.72-0.89) and the combined oral-anterior nasal swab was 0.87 (95% CI, 0.77-0.93) compared to a nasopharyngeal swab, which demonstrated a sensitivity of ˜90% when all positive tests were the reference standard. The median cycle threshold values for the SARS-CoV-2 E-gene for concordant and discordant saline gargle specimens were 17 and 31 (P < .001), for the oral swabs these values were 17 and 28 (P < .001), and for oral-anterior nasal swabs these values were 18 and 31 (P = .007).ConclusionsSelf-collected saline gargle and an oral-anterior nasal swab have a similar sensitivity to a nasopharyngeal swab for the detection of SARS-CoV-2. These alternative collection techniques are cheap and can eliminate barriers to testing, particularly in underserved populations.

| S-EPMC7870921 | biostudies-literature

Multicenter Evaluation of BioFire FilmArray Respiratory Panel 2 for Detection of Viruses and Bacteria in Nasopharyngeal Swab Samples.

Project description:The FilmArray Respiratory Panel 2 (RP2) is a multiplex in vitro diagnostic test for the simultaneous and rapid (?45-min) detection of 22 pathogens directly from nasopharyngeal swab (NPS) samples. It contains updated (and in some instances redesigned) assays that improve upon the FilmArray Respiratory Panel (RP; version 1.7), with a faster run time. The organisms identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus, human rhinovirus/enterovirus, influenza virus A, influenza virus A H1, influenza virus A H1-2009, influenza virus A H3, influenza virus B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, respiratory syncytial virus, Bordetella pertussis, Chlamydia pneumoniae, and Mycoplasma pneumoniae Two new targets are included in the FilmArray RP2: Middle East respiratory syndrome coronavirus and Bordetella parapertussis This study provides data from a multicenter evaluation of 1,612 prospectively collected NPS samples, with performance compared to that of the FilmArray RP or PCR and sequencing. The overall percent agreement between the FilmArray RP2 and the comparator testing was 99.2%. The RP2 demonstrated a positive percent agreement of 91.7% or greater for detection of all but three analytes: coronavirus OC43, B. parapertussis, and B. pertussis The FilmArray RP2 also demonstrated a negative percent agreement of ?93.8% for all analytes. Of note, the adenovirus assay detects all genotypes, with a demonstrated increase in sensitivity. The FilmArray RP2 represents a significant improvement over the FilmArray RP, with a substantially shorter run time that could aid in the diagnosis of respiratory infections in a variety of clinical scenarios.

| S-EPMC5971546 | biostudies-literature

Diagnostic accuracy of nasopharyngeal swab, nasal swab and saliva swab samples for the detection of SARS-CoV-2 using RT-PCR.

Project description:BackgroundThe current gold standard in coronavirus disease (COVID-19) diagnostics is the real-time reverse transcription-polymerase chain reaction (RT-PCR) assay for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasopharyngeal swab (NPS) samples. Alternatively, nasal swab (NS) or saliva swab (SS) specimens are used, although available data on test accuracy are limited. We examined the diagnostic accuracy of NPS/NS/SS samples for this purpose.MethodsTen patients were included after being tested positive for SARS-CoV-2 RT-PCR in NPS samples according to the National Institute of Infectious Disease guidelines. In comparison with this conventional diagnostic method, NPS/NS/SS samples were tested using the cobas 6800 systems RT-PCR device. To investigate the usefulness of the cobas method and the difference among sample types, the agreement and sensitivity were calculated. Five to six samples were collected over a total period of 5-6 d from each patient.ResultsFifty-seven sets of NPS/NS/SS samples were collected, of which 40 tested positive for COVID-19 by the conventional method. Overall, the concordance rates using the conventional method were 86.0%/70.2%/54.4% for NPS/NS/SS samples (cobas); however, for samples collected up to and including on Day 9 after disease onset (22 negative and one positive specimens), the corresponding rates were 95.7%/87.0%/65.2%. The overall sensitivity estimates were 100.0%/67.5%/37.5% for NPS/NS/SS samples (cobas). For samples up to 9 d after onset, the corresponding values were 100.0%/86.4%/63.6%.ConclusionsNS samples are more reliable than SS samples and can be an alternative to NPS samples. They can be a useful diagnostic method in the future.

| S-EPMC8006266 | biostudies-literature

Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples.

Project description:ObjectivesThe gold-standard COVID-19 diagnosis relies on detecting SARS-CoV-2 using RNA purification and one-step retrotranscription and quantitative PCR (RT-qPCR). Based on the urgent need for high-throughput screening, we tested the performance of three alternative, simple and affordable protocols to rapidly detect SARS-CoV-2, bypassing the long and tedious RNA extraction step and reducing the time to viral detection.MethodsWe evaluated three methods based on direct nasopharyngeal swab viral transmission medium (VTM) heating before the RT-qPCR: a) direct without additives; b) in a formamide-EDTA (FAE) buffer, c) in a RNAsnapTM buffer.ResultsAlthough with a delay in cycle threshold compared to the gold-standard, we found consistent results in nasopharyngeal swab samples that were subject to a direct 70°C incubation for 10 min.ConclusionsOur findings provide valuable options to overcome any supply chain issue and help to increase the throughput of diagnostic tests, thereby complementing standard diagnosis.

| S-EPMC7833505 | biostudies-literature

Nasopharyngeal swab samples

Project description:Nasopharyngeal swabs Raw sequence reads

| PRJNA752146 | ENA

Human Respiratory Syncytial Virus-Induced Immune Signature of Infection Revealed by Transcriptome Analysis of Clinical Pediatric Nasopharyngeal Swab Samples.

Project description:Human respiratory syncytial virus (HRSV) constitutes one the main causes of respiratory infection in neonates and infants worldwide. Transcriptome analysis of clinical samples using high-throughput technologies remains an important tool to better understand virus-host complex interactions in the real-life setting but also to identify new diagnosis/prognosis markers or therapeutics targets. A major challenge when exploiting clinical samples such as nasal swabs, washes, or bronchoalveolar lavages is the poor quantity and integrity of nucleic acids. In this study, we applied a tailored transcriptomics workflow to exploit nasal wash samples from children who tested positive for HRSV. Our analysis revealed a characteristic immune signature as a direct reflection of HRSV pathogenesis and highlighted putative biomarkers of interest such as IP-10, TMEM190, MCEMP1, and TIMM23.

| S-EPMC8006426 | biostudies-literature

Diagnostic performance of multiplex PCR on pulmonary samples versus nasopharyngeal aspirates in community-acquired severe lower respiratory tract infections.

Project description:BACKGROUND:PCR-based techniques for the diagnosis of community- acquired severe lower respiratory tract infections are becoming the standard of care. However, their relative ability to identify either atypical bacteria or viruses that cause LRTI from clinical samples from various sources is yet to be determined. OBJECTIVES AND STUDY DESIGN:The aim of our study was to compare the diagnostic yield of nasopharyngeal aspirates with that of pulmonary samples for the etiological diagnosis of severe acute lower respiratory tract infections by multiplex PCR. Patients were adults with community-acquired pneumonia or acute exacerbation of chronic obstructive pulmonary disease. RESULTS:We obtained concordant results for 81 (79%) of the 103 pairs of samples. In 14 of the 22 discordant results, more pathogens were evidenced in the lower respiratory tract samples. CONCLUSIONS:Pulmonary samples had a similar diagnostic sensitivity for virus detection by multiplex PCR as nasopharyngeal aspirates. In contrast, in our study, the diagnostic efficacy of pulmonary samples for Legionella pneumophila over simple aspirates was clearly superior.

| S-EPMC7185397 | biostudies-literature

Human polyomavirus type six in respiratory samples from hospitalized children with respiratory tract infections in Beijing, China.

Project description:BackgroundHPyV6 is a novel human polyomavirus (HPyV), and neither its natural history nor its prevalence in human disease is well known. Therefore, the epidemiology and phylogenetic status of HPyV6 must be systematically characterized.MethodsThe VP1 gene of HPyV6 was detected with an established TaqMan real-time PCR from nasopharyngeal aspirate specimens collected from hospitalized children with respiratory tract infections. The HPyV6-positive specimens were screened for other common respiratory viruses with real-time PCR assays.ResultsThe prevalence of HPyV6 was 1.7 % (15/887), and children ≤ 5 years of age accounted for 80 % (12/15) of cases. All 15 HPyV6-positive patients were coinfected with other respiratory viruses, of which influenza virus A (IFVA) (8/15, 53.3 %) and respiratory syncytial virus (7/15, 46.7 %) were most common. All 15 HPyV6-positive patients were diagnosed with lower respiratory tract infections, and their viral loads ranged from 1.38 to 182.42 copies/μl nasopharyngeal aspirate specimen. The most common symptoms were cough (100 %) and fever (86.7 %). The complete 4926-bp genome (BJ376 strain, GenBank accession number KM387421) was amplified and showed 100 % identity to HPyV6 strain 607a.ConclusionsThe prevalence of HPyV6 was 1.7 % in nasopharyngeal aspirate specimens from hospitalized children with respiratory tract infections, as analyzed by real-time PCR. Because the coinfection rate was high and the viral load low, it was not possible to establish a correlation between HPyV6 and respiratory diseases.

| S-EPMC4604616 | biostudies-literature

Detection of human bocavirus in Japanese children with lower respiratory tract infections.

Project description:Human bocavirus (HBoV), a newly cloned human virus of the genus Bocavirus, was detected by PCR from nasopharyngeal swab samples (8 of 318; 5.7%) collected from children with lower respiratory tract infections. HBoV may be one of the causative agents of lower respiratory tract infections in young children.

| S-EPMC1393160 | biostudies-literature

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